Same problem, I am using Manjaro Deepin and Oracle Java. When alt-tabbing a couple of things happen:
Mouse input keeps going to minecraft only; I cannot click anything.
I cannot alt-tab back into minecraft, and when I try the alt-tab menu stays on screen.
Keyboard input does go into the window on screen.
The thing I've been doing to get out of this weird behaviour is the following:
While stuck in the alt-tab screen, I look at the minecraft miniature and navigate with my mouse to the graphics options, where I disable fullscreen. After this I can alt-tab to another window, select minecraft, hit f11 and resume playing
Using the same technique, hitting quit game in the main menu, and restarting minecraft.
Hmm, that's true. I don't want to harm anyone either. If it's intended I'll close this issue.
I fixed it by relogging so I think I can't give a world download with the glitch.
But it has happend multiple times.
Having the exact same issue, with flite installed on Arch Linux.